- Update to 6.2.0

Submitted by:	Wen Heping(myself)
Approved by:	maintainer(via Email)

3 files changed, 98 insertions, 59 deletions

diff --git a/biology/embassy/Makefile b/biology/embassy/Makefile
index fc3d4588c53d..9a4f00bea333 100644
--- a/biology/embassy/Makefile
+++ b/biology/embassy/Makefile
@@ -7,10 +7,9 @@
 #
 
 PORTNAME=	embassy
-PORTVERSION=	6.0.0
-PORTREVISION=	3
+PORTVERSION=	6.2.0
 CATEGORIES=	biology
-MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/old/${PORTVERSION}/
+MASTER_SITES=	ftp://emboss.open-bio.org/pub/EMBOSS/
 DIST_SUBDIR=	emboss
 
 MAINTAINER=	fernan@iib.unsam.edu.ar
@@ -54,15 +53,15 @@ DOMAINATRIX_VERSION=	0.1.0
 EMNU_VERSION=		1.05
 ESIM4_VERSION=		1.0.0
 HMMER_VERSION=		2.3.2
-MEMENEW_VERSION=	0.1.0
-MSE_VERSION=		1.0.0
-TOPO_VERSION=		1.0.0
-PHYLIPNEW_VERSION=	3.67
+MEMENEW_VERSION=	4.0.0
+MSE_VERSION=		3.0.0
+TOPO_VERSION=		2.0.0
+PHYLIPNEW_VERSION=	3.69
 DOMALIGN_VERSION=	0.1.0
 DOMSEARCH_VERSION=	0.1.0
 SIGNATURE_VERSION=	0.1.0
 STRUCTURE_VERSION=	0.1.0
-MYEMBOSS_VERSION=	6.0.0
+MYEMBOSS_VERSION=	6.2.0
 VIENNA_VERSION=		1.7.2
 MIRA_VERSION=		2.8.2
 IPRSCAN_VERSION=	4.3.1
@@ -97,6 +96,9 @@ do-extract:
 	  fi
 .endfor
 
+post-extract:
+	@${REINPLACE_CMD} -e 's#emboss_doc##g' ${EMBASSY_WRKDIR}/MIRA-2.8.2/Makefile.in
+
 post-patch:
 	@${FIND} ${WRKSRC} -name configure | ${XARGS} ${REINPLACE_CMD} -e 's|echo aout|echo elf|'
 
diff --git a/biology/embassy/distinfo b/biology/embassy/distinfo
index d4ab628f009b..564f2279bcc6 100644
--- a/biology/embassy/distinfo
+++ b/biology/embassy/distinfo
@@ -1,51 +1,51 @@
-MD5 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 0f5211a2ee754b4f32332beaf660964c
-SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 7596e76b79f19d77e27b8ea8a75a3e1ba4c806aa548cb9675f23e2bb434a42b1
-SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 420983
-MD5 (emboss/EMNU-1.05.tar.gz) = df6c267bb12e3ecd19bffe5f678bfdb3
-SHA256 (emboss/EMNU-1.05.tar.gz) = 2f58621cc7151f813ce608dcd5b3505fc84af882c778fe28167508d6851dc333
-SIZE (emboss/EMNU-1.05.tar.gz) = 390229
-MD5 (emboss/ESIM4-1.0.0.tar.gz) = 36d9e1dc37004ff4189f583d8d3b037b
-SHA256 (emboss/ESIM4-1.0.0.tar.gz) = 219b3541e2a67d31fd62140c2c9c2b41e2d3d814dec6aaf691f764e337917577
-SIZE (emboss/ESIM4-1.0.0.tar.gz) = 431898
-MD5 (emboss/HMMER-2.3.2.tar.gz) = edc18f5515f1fd712b7d2accf58a9a2e
-SHA256 (emboss/HMMER-2.3.2.tar.gz) = 9b27f2b7a9059b017e3bd3d31de08f6fbf7d49c3e025d73abd83ff0567732258
-SIZE (emboss/HMMER-2.3.2.tar.gz) = 565686
-MD5 (emboss/MEMENEW-0.1.0.tar.gz) = 72f4a3b8544aa1603301b7b83692a133
-SHA256 (emboss/MEMENEW-0.1.0.tar.gz) = 5411d1445feb1b5e460e598a9d7e670a4357fe7aa350d96531b1aa9c79fab636
-SIZE (emboss/MEMENEW-0.1.0.tar.gz) = 450102
-MD5 (emboss/MSE-1.0.0.tar.gz) = 3122000020565077a421a53cf114127a
-SHA256 (emboss/MSE-1.0.0.tar.gz) = 9e3688ff3514b7ea6cf104fbd2a2e611fe726fb7ac4bebab6f3c103f05c08d90
-SIZE (emboss/MSE-1.0.0.tar.gz) = 445562
-MD5 (emboss/PHYLIPNEW-3.67.tar.gz) = cbd539fb39673cc362d827fa731f03f3
-SHA256 (emboss/PHYLIPNEW-3.67.tar.gz) = efbfdbff0109c62823caf13f20cb6462f54371d55899fcbbe29240e503584945
-SIZE (emboss/PHYLIPNEW-3.67.tar.gz) = 1624802
-MD5 (emboss/TOPO-1.0.0.tar.gz) = 03ea6cf067db1f673ec27195076b0e4a
-SHA256 (emboss/TOPO-1.0.0.tar.gz) = a7fd297c5e27becedd4aafd272123a176581c68b90de872fb3cb46356333cc16
-SIZE (emboss/TOPO-1.0.0.tar.gz) = 379929
-MD5 (emboss/DOMALIGN-0.1.0.tar.gz) = 58dff4731762bef6248b163bf2d160bd
-SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = c448dc461b36e299c6338f25c102de2388cc33515eae8fd1dc7097920efa409a
-SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 462156
-MD5 (emboss/DOMSEARCH-0.1.0.tar.gz) = e862f6b4f02f4640f9729862efab5a0a
-SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = fb34c1b2f668f89abe6912fe75e9828c53802820753aa8a1b952f37894939c95
-SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 470537
-MD5 (emboss/SIGNATURE-0.1.0.tar.gz) = cc7c707c41156b6681ddca7b76ff009d
-SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = 0966e165516448e214275e3cafcca91b9bb83d96264d2bf205aace1380138d2f
-SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 574940
-MD5 (emboss/STRUCTURE-0.1.0.tar.gz) = 7df40530fd15f441c531f5dbd5c10fff
-SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = cd8b17947fe764e830bd14887deb85a5f196f490d25b9c6408aaca0c1baecd23
-SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 532035
-MD5 (emboss/MYEMBOSS-6.0.0.tar.gz) = 5f51d49558131a518ac40220dd7fa0c3
-SHA256 (emboss/MYEMBOSS-6.0.0.tar.gz) = 7f24d800044b0957006c8550de74ca621301f6de1c724980fe90e8a6093b6048
-SIZE (emboss/MYEMBOSS-6.0.0.tar.gz) = 343305
-MD5 (emboss/VIENNA-1.7.2.tar.gz) = f6ec2092de41dafdb6cf302dd5412498
-SHA256 (emboss/VIENNA-1.7.2.tar.gz) = 7bed50f9992aec250f974f5c5fd9a42d49c24f05e0e9fac88bb94b2d76be25db
-SIZE (emboss/VIENNA-1.7.2.tar.gz) = 682200
-MD5 (emboss/MIRA-2.8.2.tar.gz) = c74a63e10ce983c39389593693c851e7
-SHA256 (emboss/MIRA-2.8.2.tar.gz) = 33d756bd50fe26c04aff862f34230feaad831cbe538096e4d8e5c8e0b6784fe1
-SIZE (emboss/MIRA-2.8.2.tar.gz) = 365566
-MD5 (emboss/IPRSCAN-4.3.1.tar.gz) = 8164a9b8392d29ba3bc723c1bc5da2ff
-SHA256 (emboss/IPRSCAN-4.3.1.tar.gz) = df0bdd33ea6f279ed018f4a22e686cc14ff0e9f65342177b3b9dbb2951c3636a
-SIZE (emboss/IPRSCAN-4.3.1.tar.gz) = 339939
-MD5 (emboss/CBSTOOLS-1.0.0.tar.gz) = 9352c924a8c86233fbf6dc80c58cc481
-SHA256 (emboss/CBSTOOLS-1.0.0.tar.gz) = b61b6c19d18dd3a35eef248feb92ee68bcee0e9fc99af5185deee04a17fa3693
-SIZE (emboss/CBSTOOLS-1.0.0.tar.gz) = 343812
+MD5 (emboss/DOMAINATRIX-0.1.0.tar.gz) = fae63eaa478c0864451e969793949499
+SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 53b1633d8a4fec4335ffe96fff309ef2e61b38140dad916b042522e1a48d5e02
+SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 407290
+MD5 (emboss/EMNU-1.05.tar.gz) = f43feb89e7cf68fe37375a19a2dd971b
+SHA256 (emboss/EMNU-1.05.tar.gz) = ccad2f9572b2667b2522e47aa8256b2f17e33a31f74f75991424af0c49ca651d
+SIZE (emboss/EMNU-1.05.tar.gz) = 368599
+MD5 (emboss/ESIM4-1.0.0.tar.gz) = 16f732db3f64e702b8030a41f806e50d
+SHA256 (emboss/ESIM4-1.0.0.tar.gz) = 8c02b53105f9bb95fd0acda15133ad4ac736e720df93c06ffaa6fe54b9baad10
+SIZE (emboss/ESIM4-1.0.0.tar.gz) = 406757
+MD5 (emboss/HMMER-2.3.2.tar.gz) = e83a34abdcd4ed1419db3b4a1a7bf2ff
+SHA256 (emboss/HMMER-2.3.2.tar.gz) = fd60908ffe8fea41259480701d64c3442a6a469945dbe03fdfa5677b1a3dc6a6
+SIZE (emboss/HMMER-2.3.2.tar.gz) = 559938
+MD5 (emboss/MEMENEW-4.0.0.tar.gz) = c9256d7dfebb309533369aecdbe53667
+SHA256 (emboss/MEMENEW-4.0.0.tar.gz) = f5dab1527612e060e6230f579b3243e0da2da086df7ba0e280d0efbb99d5d973
+SIZE (emboss/MEMENEW-4.0.0.tar.gz) = 507901
+MD5 (emboss/MSE-3.0.0.tar.gz) = abb377c097b841308e50a60991ad4b62
+SHA256 (emboss/MSE-3.0.0.tar.gz) = 1fc5f5313cede53ad95122afeb69b4b588f3b564567bff9855a9691b92eea701
+SIZE (emboss/MSE-3.0.0.tar.gz) = 425691
+MD5 (emboss/PHYLIPNEW-3.69.tar.gz) = af08b628e433a0561f830b21412c2969
+SHA256 (emboss/PHYLIPNEW-3.69.tar.gz) = ae0fd57a5b87961d12df8579298d5ec02a147d6678ead4b561dff2c57c5dba67
+SIZE (emboss/PHYLIPNEW-3.69.tar.gz) = 1652212
+MD5 (emboss/TOPO-2.0.0.tar.gz) = 735b6d53e6644b4033ce32f0a2591248
+SHA256 (emboss/TOPO-2.0.0.tar.gz) = 15f1106800ba803e2c5d79dbfa79b5d521e9ed0ca9da0ceaa77e15366613e915
+SIZE (emboss/TOPO-2.0.0.tar.gz) = 377565
+MD5 (emboss/DOMALIGN-0.1.0.tar.gz) = d369817f082da807ca82e8953f04c128
+SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = 33a12d28c16039663467f34d930b2a0a6ab2ef7d987db94fd8ed4abd02b1bf9f
+SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 430542
+MD5 (emboss/DOMSEARCH-0.1.0.tar.gz) = dd9d7c6be07c254c6d5487aa5678a74a
+SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = af2e408dcd29b9330df7c310d64c888f53d225ebb0bb5402237891fdcdea7ce3
+SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 447445
+MD5 (emboss/SIGNATURE-0.1.0.tar.gz) = 49cfa31d0a42e31e1141cec704bf8ac9
+SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = e24bda9ff60ef9940f603f4c65b7e5673d6b81ef0c19d53b294197e98bb2497c
+SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 559082
+MD5 (emboss/STRUCTURE-0.1.0.tar.gz) = 6edce4e40a17a6ea836f2e13620c1f86
+SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = c555e1fc16b377109a1bef21116bfe0907709fb2f629d7cbb4add455bc871050
+SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 521708
+MD5 (emboss/MYEMBOSS-6.2.0.tar.gz) = f302aafbe22d0f3e1ca6cd4280f91d21
+SHA256 (emboss/MYEMBOSS-6.2.0.tar.gz) = 13edbea0d11a14f67631a4cf6c69985f42c97383d8182f8815e294be03c5ebae
+SIZE (emboss/MYEMBOSS-6.2.0.tar.gz) = 322935
+MD5 (emboss/VIENNA-1.7.2.tar.gz) = 90bc38801dfe2d4967ed7b35070856e0
+SHA256 (emboss/VIENNA-1.7.2.tar.gz) = e2288e6a2f4538cce916033208ab12f0ffb8a92bb1d3ab89fae302b785171fb7
+SIZE (emboss/VIENNA-1.7.2.tar.gz) = 649028
+MD5 (emboss/MIRA-2.8.2.tar.gz) = f59b73667f3d212d7dbd43fed6117bd9
+SHA256 (emboss/MIRA-2.8.2.tar.gz) = 9d2a64fdb1b95bb6e2ac280be3352740e9b5f498f2ff17157374a2ca9744601d
+SIZE (emboss/MIRA-2.8.2.tar.gz) = 347282
+MD5 (emboss/IPRSCAN-4.3.1.tar.gz) = ac921ebe9555e7f939bd8a06aa524994
+SHA256 (emboss/IPRSCAN-4.3.1.tar.gz) = 179513e2473dc31e5b6153c29670773e7bceaaf84315156961baf8f1e292a289
+SIZE (emboss/IPRSCAN-4.3.1.tar.gz) = 345907
+MD5 (emboss/CBSTOOLS-1.0.0.tar.gz) = c2405d865148cdcfdccdf5623f5fa784
+SHA256 (emboss/CBSTOOLS-1.0.0.tar.gz) = 100131d86d4efeafbd63fc712c82bf493e9d174f0bc505e37bdd35ffb56182ff
+SIZE (emboss/CBSTOOLS-1.0.0.tar.gz) = 385340
diff --git a/biology/embassy/pkg-plist b/biology/embassy/pkg-plist
index 3badc2e6a7d9..ff9b9963614d 100644
--- a/biology/embassy/pkg-plist
+++ b/biology/embassy/pkg-plist
@@ -188,14 +188,18 @@
 %%PLIST_HMMER%%bin/ehmmsearch
 %%PLIST_MEMENEW%%share/EMBOSS/acd/emast.acd
 %%PLIST_MEMENEW%%share/EMBOSS/acd/ememe.acd
+%%PLIST_MEMENEW%%share/EMBOSS/acd/ememetext.acd
 %%PLIST_MEMENEW%%share/EMBOSS/doc/programs/text/emast.txt
 %%PLIST_MEMENEW%%share/EMBOSS/doc/programs/text/ememe.txt
+%%PLIST_MEMENEW%%share/EMBOSS/doc/programs/text/ememetext.txt
 %%PLIST_MEMENEW%%share/EMBOSS/doc/html/embassy/memenew/index.html
 %%PLIST_MEMENEW%%share/EMBOSS/doc/html/embassy/memenew/emast.html
 %%PLIST_MEMENEW%%share/EMBOSS/doc/html/embassy/memenew/ememe.html
+%%PLIST_MEMENEW%%share/EMBOSS/doc/html/embassy/memenew/ememetext.html
 %%PLIST_MEMENEW%%@dirrm share/EMBOSS/doc/html/embassy/memenew
 %%PLIST_MEMENEW%%bin/emast
 %%PLIST_MEMENEW%%bin/ememe
+%%PLIST_MEMENEW%%bin/ememetext
 %%PLIST_MSE%%share/EMBOSS/acd/mse.acd
 %%PLIST_MSE%%share/EMBOSS/doc/programs/text/mse.txt
 %%PLIST_MSE%%share/EMBOSS/doc/html/embassy/mse/index.html
@@ -251,11 +255,14 @@
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fcontml.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fcontrast.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdiscboot.txt
+%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdolmove.txt
+%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/frestdist.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnacomp.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnadist.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnainvar.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnaml.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnamlk.txt
+%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnamove.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnapars.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdnapenny.txt
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/programs/text/fdollop.txt
@@ -289,6 +296,9 @@
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fcontml.html
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fcontrast.html
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdiscboot.html
+%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdnamove.html
+%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdolmove.html
+%%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/frestdist.html
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdnacomp.html
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdnadist.html
 %%PLIST_PHYLIPNEW%%share/EMBOSS/doc/html/embassy/phylipnew/fdnainvar.html
@@ -374,6 +384,7 @@
 %%PLIST_TOPO%%share/EMBOSS/doc/programs/text/topo.txt
 %%PLIST_TOPO%%share/EMBOSS/doc/html/embassy/topo/index.html
 %%PLIST_TOPO%%share/EMBOSS/doc/html/embassy/topo/topo.html
+%%PLIST_TOPO%%share/EMBOSS/doc/html/embassy/topo/topo.1.topo.gif
 %%PLIST_TOPO%%@dirrm share/EMBOSS/doc/html/embassy/topo
 %%PLIST_TOPO%%bin/topo
 %%PLIST_VIENNA%%share/EMBOSS/acd/vrnaalifold.acd
@@ -451,8 +462,34 @@
 %%PLIST_MIRA%%share/EMBOSS/acd/emiraest.acd
 %%PLIST_MIRA%%bin/emira
 %%PLIST_MIRA%%bin/emiraest
+%%PLIST_MYEMBOSS%%share/EMBOSS/doc/html/embassy/myemboss/index.html
+%%PLIST_MYEMBOSS%%@dirrm share/EMBOSS/doc/html/embassy/myemboss
 %%PLIST_IPRSCAN%%share/EMBOSS/acd/eiprscan.acd
+%%PLIST_IPRSCAN%%share/EMBOSS/doc/html/embassy/iprscan/eiprscan.html
+%%PLIST_IPRSCAN%%share/EMBOSS/doc/html/embassy/iprscan/index.html
 %%PLIST_IPRSCAN%%bin/eiprscan
+%%PLIST_IPRSCAN%%@dirrm share/EMBOSS/doc/html/embassy/iprscan
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/elipop.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/eiprscan.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/echlorop.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/enetnglyc.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/enetoglyc.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/enetphos.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/eprop.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/esignalp.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/etmhmm.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/programs/text/eyinoyang.txt
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/index.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/echlorop.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/elipop.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/enetnglyc.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/enetoglyc.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/enetphos.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/eprop.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/esignalp.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/etmhmm.html
+%%PLIST_CBSTOOLS%%share/EMBOSS/doc/html/embassy/cbstools/eyinoyang.html
+%%PLIST_CBSTOOLS%%@dirrm share/EMBOSS/doc/html/embassy/cbstools
 %%PLIST_CBSTOOLS%%share/EMBOSS/acd/echlorop.acd
 %%PLIST_CBSTOOLS%%share/EMBOSS/acd/elipop.acd
 %%PLIST_CBSTOOLS%%share/EMBOSS/acd/enetnglyc.acd